Veupathdb Tools

Configuration File: veupathdb_tools.json Tool Type: Local Tools Count: 3

This page contains all tools defined in the veupathdb_tools.json configuration file.

Available Tools

VEuPathDB_list_gene_searches (Type: BaseRESTTool)

List all available gene search strategies in VEuPathDB. Returns the search types that can be used…

VEuPathDB_list_gene_searches tool specification

Tool Information:

  • Name: VEuPathDB_list_gene_searches

  • Type: BaseRESTTool

  • Description: List all available gene search strategies in VEuPathDB. Returns the search types that can be used to query genes across pathogen, vector, and host genomes. Each search has a URL segment, display name, description, and the parameters it accepts. Common searches include: GenesByTaxonGene (by organism), GenesFromTranscripts (transform transcript results to genes), and single gene lookups. Use this to discover what types of gene queries are available before constructing searches.

Parameters:

No parameters required.

Example Usage:

query = {
    "name": "VEuPathDB_list_gene_searches",
    "arguments": {
    }
}
result = tu.run(query)

VEuPathDB_list_organism_searches (Type: BaseRESTTool)

List all available organism search strategies in VEuPathDB. Returns the search types that can be …

VEuPathDB_list_organism_searches tool specification

Tool Information:

  • Name: VEuPathDB_list_organism_searches

  • Type: BaseRESTTool

  • Description: List all available organism search strategies in VEuPathDB. Returns the search types that can be used to query organisms in the VEuPathDB database, covering 785+ pathogen, vector, and host organism genomes. Useful for discovering what organism queries are available. Common searches include: AllOrganisms (list all), GenomeDataTypes (genome statistics), GeneMetrics (gene counts), and OrganismsByText (text search).

Parameters:

No parameters required.

Example Usage:

query = {
    "name": "VEuPathDB_list_organism_searches",
    "arguments": {
    }
}
result = tu.run(query)

VEuPathDB_list_record_types (Type: BaseRESTTool)

List all available record types in VEuPathDB (Eukaryotic Pathogen, Vector and Host Informatics Re…

VEuPathDB_list_record_types tool specification

Tool Information:

  • Name: VEuPathDB_list_record_types

  • Type: BaseRESTTool

  • Description: List all available record types in VEuPathDB (Eukaryotic Pathogen, Vector and Host Informatics Resources). VEuPathDB is a unified bioinformatics resource for eukaryotic pathogen and host genomics covering Plasmodium (malaria), Toxoplasma, Cryptosporidium, Trypanosoma, Leishmania, fungi, and vector organisms. Returns the available record types (gene, transcript, organism, genomic-sequence, etc.) that can be queried through VEuPathDB’s search API. Encompasses sub-databases: PlasmoDB, ToxoDB, CryptoDB, TriTrypDB, FungiDB, AmoebaDB, MicrosporidiaDB, PiroplasmaDB, GiardiaDB, TrichDB, HostDB, VectorBase, and SchistoDB.

Parameters:

No parameters required.

Example Usage:

query = {
    "name": "VEuPathDB_list_record_types",
    "arguments": {
    }
}
result = tu.run(query)